short length amino acids

Question

[desptsp]

Hello! I have two sequences of amino acids 60 aa each , and I want to compare them and I'm supposed to do that with Blast. Can anybody help me how to blast them locally ? Moreover does anybody know bibliography which prooves which alignment is the best for short length amico acids ( i think global is preferable). Thank you very much

[Sej Modha]

It is a bit difficult to guess what you mean by "compare them" without the knowledge of what these sequences are.

You could try pairwise sequence alignment tools available online:

https://www.ebi.ac.uk/Tools/psa/

[desptsp]

I have to practice alignment between short-length amino acids sequence with blast and I'm trying to find similarity and identity . For example I downloaded two sequences of Homo sapiens and Homo sapiens neanderthal

[GenoMax]

Can anybody help me how to blast them locally ?

You can install blast program locally and use that. BLAST Handbook from NCBI: https://www.ncbi.nlm.nih.gov/books/NBK279690/

BLAST is a local aligner so if you want to do global alignments then you may want to look at other options like Needleman-Wunsch especially if you are looking to align only two sequences.